actions_group is neither in stable nor in default branch of galaxy-dist repository, it's present only in galaxy-central.
Nicola Il giorno lun, 07/10/2013 alle 11.24 -0400, Dave Bouvier ha scritto: > Peter, > > The platform detection code is not yet in the stable branch, but is > intended to be included in the upcoming release. The automated testing > framework does run the default branch, though, so the nightly tests will > make use of the new definitions. > > --Dave B. > > On 10/07/2013 11:22 AM, Peter Cock wrote: > > On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock <p.j.a.c...@googlemail.com> > > wrote: > >> On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier <d...@bx.psu.edu> wrote: > >>> Peter, > >>> > >>> I did some investigating, and it turns out that the if [[ condition ]] > >>> syntax used in the ncbi tool dependency is only compatible with bash, not > >>> sh. > >> > >> Does that mean the test system has switched between sh and bash > >> and back to sh again? > > > > Is there anything written down about the expected shell(s) > > available for a standard Galaxy instance? > > > >>> For sh, the corresponding syntax would look like: > >>> > >>> if [ "$string" = "value" ] > >>> then > >>> echo "string is equal to value" > >>> fi > >>> > >>> However, it strikes me that the platform detection and download url > >>> determination could also be done using the recently introduced > >>> <actions_group> feature, which would bypass shell-dependent > >>> conditional syntax entirely. > >> > >> Yes, but is that in stable releases for galaxy-dist yet? > > > > In the meantime I will try that on the Test Tool Shed, based > > on the tool_dependencies.xml example you shared before: > > > > http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26/c83440a9bdfb > > > > Note there seems to me to be a lot of duplication - I would like > > a way to unambiguously combine multiple CPU architectures > > into a single action. > > > > For example, combine these: > > > > <actions os="darwin" architecture="x86_64"> > > <actions os="darwin" architecture="i386"> > > > > into: > > > > <actions os="darwin" architecture="x86_64,i386"> > > > > or just: > > > > <actions os="darwin"> > > > > and similarly, combine these: > > > > <actions os="linux" architecture="i386"> > > <actions os="linux" architecture="i686"> > > > > into something like: > > > > <actions os="linux" architecture="i386,i686"> > > > > Assuming that works on the Test Tool Shed, and the code for > > this is already in the stable releases, I will update the main > > Tool Shed definition as well. > > > > Thanks, > > > > Peter > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
